This article is from the In-Depth Report The Food Issue: The Science of Feast, Fuel and Farm

Microbes Help Grow Better Crops

Enlisting bacteria and fungi from the soil to support crop plants is a promising alternative to the heavy use of fertilizer and pesticides

Don Foley

In Brief

  • Microbes in and around food crops do not just cause human disease. In certain cases, they do exactly the opposite, acting as sentinels of food safety and furnishing an environmentally sound alternative to massive inputs of fertilizers and pesticides.
  • Spreading bacteria on crops became a strategy for researchers in Virginia who sprayed anti-Salmonella soil bacteria on tomato seedlings. The scientists hope the approach might prevent annual outbreaks of food poisoning from raw tomatoes grown on the East Coast.
  • Applying fungi to cassava plants, a project of researchers in Colombia, helps the roots acquire phosphate without the need for expensive fertilizers, a boon in tropical nations where the amount of nutrient that can be obtained from the soil is particularly low.

More on this Topic

Tomatoes fresh from a roadside stand, sliced, glistening, and served with nothing more than salt, pepper and a drizzle of olive oil—a sacred pleasure of summer. To die for? Possibly so.

Almost every year for the past decade or so, public health investigators on the East Coast have tracked down one or two Salmonella outbreaks and identified local tomatoes as the culprit. These outbreaks are typically small, affecting 10 to 100 people. Yet for the very old and very young, they can mean hospitalization and even death.

A few years ago Eric Brown, director of microbiology at the U.S. Food and Drug Administration's Center for Food Safety and Applied Nutrition, began to wonder: Why East Coast tomatoes? The Salmonella bug probably gets onto tomato fields from surface water and the droppings of seagulls, turtles, poultry, and other animals. So why aren't West Coast tomatoes contaminated, too?

The answer to Brown's question came from a close inspection of the community of bacteria, viruses and fungi living in and around all plants—what scientists call the microbiome. West Coast tomatoes, it turned out, grow in the company of soil bacteria that inhibit and even kill Salmonella. When researchers went to hunt for similar strains back East, they found them but in smaller numbers. Thus, in a pilot study in Virginia, the fda has been brewing up populations of one of these local bacteria, Paenibacillus, spraying them onto tomato seedlings and getting the same anti-Salmonella effect on the crop. Brown expects to move the process out to commercial tomato growers in 2014 or 2015.

Adding bacteria to a crop to prevent human disease could be the start of a whole new path to food safety, possibly extending beyond tomatoes to cantaloupes, spinach, sprouts and other crops that have made Salmonella and Escherichia coli headlines. The tomato project fits into a far more dramatic shift in how we grow our food, based on a new understanding of microbes in the soil and of the many ways plants and microbes depend on one another.

It is almost the opposite of the green revolution, which dramatically boosted agricultural productivity in the mid-20th century with massive inputs of fertilizer, pesticides and water. The microbial revolution aims instead to take advantage of what is already there: as many as 40,000 microbe species in a gram of soil. Until recently, this microbial community—what might be called the “agribiome”—was largely a mystery. But over the past decade low-cost DNA sequencing and other technologies have opened up the secret world of microbes. Botanists can now identify every member of the microbial community that surrounds a plant. By doing so, they have begun to understand how various microbes behave in different seasons and soil environments and have even started devising ways to tweak them to help plants grow better.

Soil scientists must come to grips with so much new information, in fact, that Andrea Ottesen, the fda microbiologist who cracked the tomato Salmonella case, describes it, with a sigh, as “kind of a huge rabbit's hole at this point.” But sorting out that wealth of new information to help farmers grow better crops seems particularly urgent, given the vast challenges that agriculture now faces: the global water shortage; extreme and unpredictable weather events such as last summer's devastating drought in the U.S. corn belt; worries over the sustainability of nitrogen fertilizer produced with fossil fuels; and the prospect of having to feed an extra two billion people by midcentury.

New research suggests that microbes could provide an alternative to existing agricultural methods and genetic engineering in alleviating some of these problems. For instance, sunflowers and some other plants naturally produce the sugar trehalose, which helps to stabilize plant cell membranes and to reduce the damage from cycles of drying followed by rehydration. Other plants, including corn and potatoes, have been genetically engineered to manufacture trehalose. Yet molecular biologist Gabriel Iturriaga in Mexico hopes to eventually treat crops without any genetic modification by using the trehalose-producing bacterium Rhizobium etli, which is found around the roots of bean plants. An earlier experiment with a genetically altered version of the bacterium improved yields by 50 percent in normal conditions—and saved half the crop during a drought.

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This article was originally published with the title "Super Dirt."

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